This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Protein Tool Box is a suite of software modules develop to help the work flow around database search of product-ion spectra. It has modules that prepare the spectra for search, create customized databases, and modules for analysis of database search results. The components are modular and are used in more than one program. It also includes utilities for handling and creation of data to be used by other programs.